FAIRMol

NMT-TY0371

Pose ID 8356 Compound 515 Pose 226

DB SELECTIONDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T13
T. brucei ODC (Active site) T. brucei Active site
Ligand NMT-TY0371
PDB1F3T↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
44.1 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.68, Jaccard 0.62, H-bond role recall 0.43
Burial
82%
Hydrophobic fit
68%
Reason: strain 44.1 kcal/mol
strain ΔE 44.1 kcal/mol 3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.350 kcal/mol/HA) ✓ Good fit quality (FQ -11.29) ✓ Strong H-bond network (14 bonds) ✓ Deep burial (82% SASA buried) ✓ Lipophilic contacts well-matched (68%) ✗ Extreme strain energy (44.1 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-26.994
kcal/mol
LE
-1.350
kcal/mol/HA
Fit Quality
-11.29
FQ (Leeson)
HAC
20
heavy atoms
MW
296
Da
LogP
-0.68
cLogP
Strain ΔE
44.1 kcal/mol
SASA buried
82%
Lipo contact
68% BSA apolar/total
SASA unbound
493 Ų
Apolar buried
276 Ų

Interaction summary

HB 14 HY 2 PI 2 CLASH 3
Final rank4.299Score-26.994
Inter norm-1.396Intra norm0.046
Top1000noExcludedno
Contacts15H-bonds14
Artifact reasongeometry warning; 7 clashes; 3 protein clashes; high strain Δ 44.1
Residues
ALA67 ARG277 ASP332 ASP88 GLU274 GLY199 GLY236 GLY237 GLY276 HIS197 HIS333 LYS69 SER200 TYR331 TYR389

Protein summary

411 residues
Protein targetT13Atoms6340
Residues411Chains1
Residue summaryVAL:624; LEU:551; LYS:506; ARG:480; PHE:460; ILE:418; ASP:348; GLU:332; THR:322; TYR:315; PRO:308; ALA:290; SER:264; GLY:224; ASN:210; GLN:170

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name1F3TContacts19
PoseOpen native poseHB0
IFP residues
ALA111 ALA67 ARG154 ARG277 ASP332 ASP88 CYS70 GLU274 GLY236 GLY237 GLY276 HIS197 LYS69 PHE238 PRO275 SER200 TYR278 TYR331 TYR389
Current overlap13Native recall0.68
Jaccard0.62RMSD-
HB strict4Strict recall0.44
HB same residue+role3HB role recall0.43
HB same residue3HB residue recall0.43

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
291 1.1342832901296953 -1.47243 -28.1213 7 13 0 0.00 0.00 - no Open
308 1.1407956598243199 -1.47271 -28.0966 7 13 0 0.00 0.00 - no Open
287 1.425854450107728 -1.57638 -29.017 10 15 0 0.00 0.00 - no Open
294 1.4368563653499584 -1.58614 -29.0417 10 15 0 0.00 0.00 - no Open
340 1.5199875327590986 -1.30421 -24.1616 12 16 0 0.00 0.00 - no Open
325 1.8929444358902847 -1.09972 -20.59 10 11 0 0.00 0.00 - no Open
264 2.0213778030470935 -1.28263 -24.1424 8 15 0 0.00 0.00 - no Open
272 2.07930378903586 -1.19931 -21.6886 10 17 0 0.00 0.00 - no Open
288 2.272686469792997 -1.20072 -21.8379 10 17 0 0.00 0.00 - no Open
255 2.604134178216891 -1.55444 -29.5672 11 18 0 0.00 0.00 - no Open
395 2.618228131873109 -1.34198 -25.4179 10 16 0 0.00 0.00 - no Open
307 2.6395815071657873 -1.216 -22.6881 12 17 0 0.00 0.00 - no Open
324 2.719858307570968 -0.962258 -19.339 7 11 0 0.00 0.00 - no Open
272 2.890185804928903 -1.24872 -23.3539 7 15 0 0.00 0.00 - no Open
354 2.894301988851109 -1.46517 -27.278 13 19 0 0.00 0.00 - no Open
248 2.9955573621189955 -1.44392 -27.8137 14 18 15 0.79 0.43 - no Open
346 3.086475756889026 -1.42333 -26.6003 13 19 0 0.00 0.00 - no Open
299 3.1992481359795537 -1.24642 -23.7166 13 17 0 0.00 0.00 - no Open
285 3.2187089349618714 -1.29682 -23.427 10 17 0 0.00 0.00 - no Open
379 3.2560466957189305 -1.35838 -25.6607 9 16 1 0.05 0.00 - no Open
369 3.4560880962334983 -1.32647 -25.5936 9 16 1 0.05 0.00 - no Open
254 3.4642926757389616 -1.30203 -24.5606 9 15 0 0.00 0.00 - no Open
406 3.67636034041161 -1.29246 -24.4616 10 16 0 0.00 0.00 - no Open
333 3.717795610400825 -1.4146 -26.5109 10 14 0 0.00 0.00 - no Open
241 3.724783035797209 -1.26416 -21.7498 15 13 0 0.00 0.00 - no Open
251 3.7829044977730146 -1.35705 -25.1409 11 19 0 0.00 0.00 - no Open
330 3.7929991462566486 -0.942708 -18.8834 6 11 0 0.00 0.00 - no Open
241 4.010694369049239 -1.38136 -25.2742 11 19 0 0.00 0.00 - no Open
226 4.299065349056032 -1.39557 -26.9943 14 15 13 0.68 0.43 - no Current
257 4.359761779337785 -1.65662 -30.294 16 22 0 0.00 0.00 - no Open
274 4.532558280468934 -1.63443 -31.073 16 21 0 0.00 0.00 - no Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -26.994kcal/mol
Ligand efficiency (LE) -1.3497kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.295
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 20HA

Physicochemical properties
Molecular weight 296.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.68
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 44.10kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -82.47kcal/mol
Minimised FF energy -126.57kcal/mol

SASA & burial

✓ computed
SASA (unbound) 492.6Ų
Total solvent-accessible surface area of free ligand
BSA total 404.8Ų
Buried surface area upon binding
BSA apolar 276.1Ų
Hydrophobic contacts buried
BSA polar 128.6Ų
Polar contacts buried
Fraction buried 82.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 68.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2409.8Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1385.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)